GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Pseudomonas fluorescens FW300-N2E3

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate AO353_25695 AO353_25695 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_25695
          Length = 554

 Score =  273 bits (698), Expect = 1e-77
 Identities = 178/512 (34%), Positives = 277/512 (54%), Gaps = 27/512 (5%)

Query: 76  AFWWIDGNGEELRWSFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACL 135
           A +W   +G    ++F +L   + +FAN L  A  +++GD+V  +LP+  E  +   A  
Sbjct: 45  ALFWEGRDGASATYTFSDLQDKAARFANFLL-AQGVKKGDKVAGLLPRNVELLIVVFATW 103

Query: 136 RTGTVLIPGTTQLTQKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHS 195
           R G V  P  T    K I +RL SS A  ++TD    P ++ VA          IV+   
Sbjct: 104 RIGAVYQPLFTAFGPKAIEHRLNSSGAAVVVTDAVNRPKLNDVA------DCPTIVTVGG 157

Query: 196 REGWGNLK-------EMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPKMIGHTHSSFGL 248
            +G G ++       E+  Y++     +    D  + + FTSGTTGP K +     +  +
Sbjct: 158 PKGQGIVRGDFSFWAELPNYSAQCEPVLLDGEDPFL-LMFTSGTTGPSKALSVPLKAI-V 215

Query: 249 GLSVNGRFWLDLIASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQT 308
                 R  +DL   D  WN +D GWA   +  V  P + G  +  +  P F   S  + 
Sbjct: 216 AFQSYTRDAVDLRPEDAFWNVADPGWAYGIYFGVTGPLSMGHPITFYDGP-FTLESTCRV 274

Query: 309 LSKFPITVFCSAPTAYRMLVQ--NDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDI 366
           ++K+ IT    +PTAYR+L+   ++ +      L+   SAGEP+NPEV+  +    G+ I
Sbjct: 275 INKYGITNLTGSPTAYRLLIAGGDEFARSIKGKLRIVSSAGEPLNPEVIRWFADNLGVVI 334

Query: 367 YEGYGQTETVLICGNFKGMK--IKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVL 424
           ++ YGQTE  ++  N  G++  +  G+ G  SP   + +LDE    L  GQ G +A+   
Sbjct: 335 HDHYGQTELGMVLCNHHGLEHSVHVGAAGFASPGHRIVVLDEAYNELSVGQPGILAID-R 393

Query: 425 PERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGP 484
            + P   F  Y   P+K      G++Y++GD   ++ DG   FV RSDD+I +SGYR+GP
Sbjct: 394 TQSPMCWFAGYEGAPTKA---FVGNYYLSGDTVELNPDGSISFVGRSDDVITTSGYRVGP 450

Query: 485 FEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTT 544
           F+VESALIEHP++ E+AV+  PDP R E+VKAF+VL+  Y++    +L +E+++HV+K  
Sbjct: 451 FDVESALIEHPAVVEAAVIGKPDPERTELVKAFVVLSAQYRA--SPELAEELRQHVRKRL 508

Query: 545 APYKYPRKVEFIEELPKTVSGKVKRNELRKKE 576
           A + YPR++EF+ ELPKT SGK++R  LR +E
Sbjct: 509 AAHSYPREIEFVSELPKTPSGKLQRFILRNQE 540


Lambda     K      H
   0.319    0.134    0.416 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 750
Number of extensions: 48
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 580
Length of database: 554
Length adjustment: 36
Effective length of query: 544
Effective length of database: 518
Effective search space:   281792
Effective search space used:   281792
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory